Preheat the oven to 375 degrees F. Lightly oil a 13-by-9-by-2-inch glass baking dish.
Arrange the fennel in the baking dish. Sprinkle with the salt, lemon zest and garlic. Top with the Parmesan and drizzle with the oil. Bake until the fennel is fork-tender and golden brown, about 45 minutes.
Chop enough of the reserved fennel fronds to equal 2 teaspoons. Sprinkle the roasted fennel with the chopped fronds and the pomegranate seeds.